With the performance of PC (Personal Computer) being improved obviously, HCI (Human Computer Interface) is developing more humanely, natural and intelligent. PUI(Pen-based User Interface), as the main interface style of Post WIMP (Window + Icon + Menu + Pointing Devices) interface style, is to be the focus of research of HCI. PUI, based on pen-paper metaphor, provides a natural and highly efficient interactive mode to users, so it can reduce users' cognition burden. With the wide spread use of PUI in different fields, the usability problems of PUI are exposed gradually. Although the Usability research of PUI plays a great role in the popularity of Pen-based System, it has not drawn great attention. This paper firstly provides a global and systematical analysis of PUI, after introducing PUI history and actuality, direction of development of PUI are discussed. Secondly, this paper brings forward the usability theory of PUI. Finally, this paper puts forward the design and usability evaluation of a pen-based user interface. This paper describes author' s innovation in the research work in detail as follows: The author provides the analysis of the fundamental theory of research on the usability of pen-based user interface After the analysis of the merits and shortcomings of pen-based user interface, the author gives the principle of designing PUI. This paper provides a PUI paradigm based on user interface usability principle. It also provides the implementation of PenOffice system based on the new paradigm. The author designed and conducted the usability evaluation of PenOffice system using GOMS model.